Tourette Syndrome (TS) is a disorder of the developing telencephalon for which no significant causative genetic variant has yet emerged through the examination of blood samples. In this proposal we investigate whether somatic mutations might underlie in part the pathogenesis of TS. Existing evidence suggests that cells accumulate somatic mutations after the formation of the zygote, implying that cells of the human body do not have identical DNA sequence. Besides single nucleotide variation (SNV) and small insertion/deletions (InDels), cells can accumulate copy number variations (CNVs, i.e., duplications and deletions), insertions of transposable elements, inversions and translocations, all involving from few hundred to several millions of nucleotides. Somatic mosaicism arising in brain cells could explain the failure to discover consistent, replicable genetic risk factors in neuropsychiatric disorders like TS, and underlie at least in part the frequently observed variability between blood genotype and overall phenotype. There is no estimate of somatic mosaicism in either normal development or in disease. To test the hypothesis that somatic mutations might underlie the emergence of TS, in this proposal we will discover and quantify somatic genome variation in TS and normal control brains, followed by exploration of potential functional consequences of this variation. In Aim 1, we will perform using advanced sequencing techniques comprehensive discovery of lineage-specific and region-specific somatic genomic variations: SNVs, InDels, CNVs, retrotransposon insertions, inversion and translocations. The analysis will involve 20 TS brains and matched 20 normal control brains. Mosaic variants will be discovered and validated in prefrontal cortex (PFC), premotor cortex (PMC) and striatum (STR), three regions strongly implicated in TS, as well as in specific cell lineages isolated from these regions, including pyramidal neurons, medium spiny neurons, interneurons and microglial cells. In Aim 2, we will select 10 genomic variants, engineer them into iPSCs and in transgenic mice using CRISPR technologies, and characterize their impact on the molecular, tissue and behavior level. Together, these specific aims will provide the first estimate of somatic genomic variation (number, type, frequency) in the brain of TS and will yield hypotheses about their significance for brain development.